analyzers

analyzers

Define analyzers, which are used to track variables when the sim is run.

Analyzers typically include things like additional tracking states by age or another conditional.

Classes

Name	Description
Analyzer	Base class for Analyzers. Analyzers are used to provide more detailed information
dynamics_by_age	Example analyzer: track dynamics of a state by age.
infection_log	Log infections – see ss.InfectionLog for detail

Analyzer

analyzers.Analyzer(name=None, label=None, **kwargs)

Base class for Analyzers. Analyzers are used to provide more detailed information about a simulation than is available by default – for example, pulling states out of sim.people on a particular timestep before they get updated on the next step.

The key method of the analyzer is step(), which is called with the sim on each timestep.

dynamics_by_age

analyzers.dynamics_by_age(state, age_bins=(0, 20, 40, 100))

Example analyzer: track dynamics of a state by age.

Parameters

Name	Type	Description	Default
state	str	the name of the state to analyze	required
age_bins	list	the list of age bins to analyze by	(0, 20, 40, 100)

Examples

by_age = ss.dynamics_by_age('sis.infected')

sim = ss.Sim(diseases='sis', networks='random', analyzers=by_age)
sim.run()
sim.analyzers[0].plot() # Note: if Sim(copy_inputs=False), we can also use by_age.plot()

Methods

Name	Description
finalize_results	Convert per-step lists to arrays
init_post	Validate that the requested state exists
plot	Plot counts by age bin over time
step	Record counts of agents in each age bin who have the tracked state active

finalize_results

analyzers.dynamics_by_age.finalize_results()

Convert per-step lists to arrays

init_post

analyzers.dynamics_by_age.init_post()

Validate that the requested state exists

plot

analyzers.dynamics_by_age.plot(**kwargs)

Plot counts by age bin over time

step

analyzers.dynamics_by_age.step()

Record counts of agents in each age bin who have the tracked state active

infection_log

analyzers.infection_log()

Log infections – see ss.InfectionLog for detail

This analyzer activates an infection log running in each disease. This is different than other analyzers, but is required since the information required to create an infection log isn’t kept outside of the disease’s infect() step.

Examples

import starsim as ss
sim = ss.Sim(n_agents=1000, dt=0.2, dur=15, diseases='sir', networks='random', analyzers='infection_log')
sim.run()
sim.analyzers[0].plot()

Methods

Name	Description
animate	Animate the infection log – mostly for amusement!
finalize_results	Collect the infection logs from each of the diseases
plot	Plot all of the infection logs
step	Handled by ss.InfectionLog()

animate

analyzers.infection_log.animate(
    key=0,
    framerate=10,
    clear=False,
    cmap='parula',
    **kwargs,
)

Animate the infection log – mostly for amusement!

Parameters

Name	Type	Description	Default
key	int / str	which disease to animate the infection log of	0
framerate	float	how many frames per second to display	10
clear	bool	whether to clear the frame on each step	False
cmap	str	the colormap to use	'parula'

finalize_results

analyzers.infection_log.finalize_results()

Collect the infection logs from each of the diseases

plot

analyzers.infection_log.plot(**kwargs)

Plot all of the infection logs

step

analyzers.infection_log.step()

Handled by ss.InfectionLog()